Discovery and Optimization of New Benzimidazole- and Benzoxazole-Pyrimidone Selective PI3KBeta Inhibitors for the Treatment of Phosphatase and TENsin homologue (PTEN)-Deficient Cancers

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.252 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Discovery and Optimization of New Benzimidazole- and Benzoxazole-Pyrimidone Selective Pi3Kbeta Inhibitors for the Treatment of Phosphatase and Tensin Homologue (Pten)-Deficient Cancers.

Certal, V.Halley, F.Virone-Oddos, A.Delorme, C.Karlsson, A.Rak, A.Thompson, F.Filoche-Romm, B.El-Ahmad, Y.Carry, J.C.Abecassis, P.Y.Lejeune, P.Vincent, L.Bonnevaux, H.Nicolas, J.P.Bertrand, T.Marquette, J.P.Michot, N.Benard, T.Below, P.Vade, I.Chatreaux, F.Lebourg, G.Pilorge, F.Angouillant-Boniface, O.Louboutin, A.Lengauer, C.Schio, L.

(2012) J Med Chem 55: 4788

  • DOI: https://doi.org/10.1021/jm300241b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Most of the phosphoinositide-3 kinase (PI3K) kinase inhibitors currently in clinical trials for cancer treatment exhibit pan PI3K isoform profiles. Single PI3K isoforms differentially control tumorigenesis, and PI3Kβ has emerged as the isoform involved in the tumorigenicity of PTEN-deficient tumors. Herein we describe the discovery and optimization of a new series of benzimidazole- and benzoxazole-pyrimidones as small molecular mass PI3Kβ-selective inhibitors. Starting with compound 5 obtained from a one-pot reaction via a novel intermediate 1, medicinal chemistry optimization led to the discovery of compound 8, which showed a significant activity and selectivity for PI3Kβ and adequate in vitro pharmacokinetic properties. The X-ray costructure of compound 8 in PI3Kδ showed key interactions and structural features supporting the observed PI3Kβ isoform selectivity. Compound 8 achieved sustained target modulation and tumor growth delay at well tolerated doses when administered orally to SCID mice implanted with PTEN-deficient human tumor xenografts.

  • Organizational Affiliation

    Oncology Drug Discovery, Sanofi Research & Development , 13 quai Jules Guesde, 94403 Vitry-sur-Seine, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
934Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: (PDB Primary Data), (UniProt)
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35904
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VWN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H19 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
VWN PDBBind:  4AJW IC50: 1395 (nM) from 1 assay(s)
BindingDB:  4AJW IC50: min: 1395, max: 2655 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.4α = 90
b = 220.47β = 113.87
c = 78.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Other
  • Version 1.2: 2017-03-29
    Changes: Structure summary
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy